This has been a mystery to me for a while, and for some reason Google didn\'t help me, so let me ask.
EDIT: ok, I understand the GFM is everywhere in GitHub, and wh
github flavored markdown is used on:
and minimally on comments (commit, pull requests, etc)
a note about issues: it seems like it uses a limited version of GFM than on wiki pages or readme files.
Contrary to the other answers, GFM is only used where text is only entered through the GitHub website, not in README.md and not on GitHub Wikis.
From https://help.github.com/articles/github-flavored-markdown (emphasis added)
GitHub uses what we're calling "GitHub Flavored Markdown" (GFM) for messages, issues, and comments.
The reasoning behind this is that README.md and Wikis are part of Git repositories, and therefore can be cloned outside of the site, where one would reasonably expect (standard) Markdown rather than GFM.
For more on GitHub's rationale, see https://github.com/github/markup/issues/208#issuecomment-24927799
Edit:
Syntax highlighting (Pygments) is separate from GFM, in that, GFM employs syntax highlighting, however the presence of syntax highlighting does not entail GFM, hence why GitHub Pages will use standard Markdown line-breaks: it uses Pygments, but not GFM.
It's used when you display your README.md file on your repository front page, for example. Also, when you add comments it's GFM.